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Zhang L, Rahman J, Chung M, Lashua L, Gordon A, Balmaseda A, Kuan G, Bonneau R, Ghedin E. CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection. MICROBIOME 2023; 11:136. [PMID: 37330554 PMCID: PMC10276449 DOI: 10.1186/s40168-023-01568-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 05/05/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Disruption of the microbial community in the respiratory tract due to infections, like influenza, could impact transmission of bacterial pathogens. Using samples from a household study, we determined whether metagenomic-type analyses of the microbiome provide the resolution necessary to track transmission of airway bacteria. Microbiome studies have shown that the microbial community across various body sites tends to be more similar between individuals who cohabit in the same household than between individuals from different households. We tested whether there was increased sharing of bacteria from the airways within households with influenza infections as compared to control households with no influenza. RESULTS We obtained 221 respiratory samples that were collected from 54 individuals at 4 to 5 time points across 10 households, with and without influenza infection, in Managua, Nicaragua. From these samples, we generated metagenomic (whole genome shotgun sequencing) datasets to profile microbial taxonomy. Overall, specific bacteria and phages were differentially abundant between influenza positive households and control (no influenza infection) households, with bacteria like Rothia, and phages like Staphylococcus P68virus that were significantly enriched in the influenza-positive households. We identified CRISPR spacers detected in the metagenomic sequence reads and used these to track bacteria transmission within and across households. We observed a clear sharing of bacterial commensals and pathobionts, such as Rothia, Neisseria, and Prevotella, within and between households. However, due to the relatively small number of households in our study, we could not determine if there was a correlation between increased bacterial transmission and influenza infection. CONCLUSION We observed that airway microbial composition differences across households were associated with what appeared to be different susceptibility to influenza infection. We also demonstrate that CRISPR spacers from the whole microbial community can be used as markers to study bacterial transmission between individuals. Although additional evidence is needed to study transmission of specific bacterial strains, we observed sharing of respiratory commensals and pathobionts within and across households. Video Abstract.
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Affiliation(s)
- Lingdi Zhang
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Jahan Rahman
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Matthew Chung
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institutes of Health, NIH, Bethesda, MD, 20894, USA
| | - Lauren Lashua
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Angel Balmaseda
- Sustainable Sciences Institute, Managua, Nicaragua
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico Y Referencia, Ministry of Health, Managua, Nicaragua
| | - Guillermina Kuan
- Sustainable Sciences Institute, Managua, Nicaragua
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA.
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA.
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Lam TJ, Mortensen K, Ye Y. Diversity and dynamics of the CRISPR-Cas systems associated with Bacteroides fragilis in human population. BMC Genomics 2022; 23:573. [PMID: 35953824 PMCID: PMC9367070 DOI: 10.1186/s12864-022-08770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/15/2022] [Indexed: 11/22/2022] Open
Abstract
Background CRISPR-Cas (clustered regularly interspaced short palindromic repeats—CRISPR-associated proteins) systems are adaptive immune systems commonly found in prokaryotes that provide sequence-specific defense against invading mobile genetic elements (MGEs). The memory of these immunological encounters are stored in CRISPR arrays, where spacer sequences record the identity and history of past invaders. Analyzing such CRISPR arrays provide insights into the dynamics of CRISPR-Cas systems and the adaptation of their host bacteria to rapidly changing environments such as the human gut. Results In this study, we utilized 601 publicly available Bacteroides fragilis genome isolates from 12 healthy individuals, 6 of which include longitudinal observations, and 222 available B. fragilis reference genomes to update the understanding of B. fragilis CRISPR-Cas dynamics and their differential activities. Analysis of longitudinal genomic data showed that some CRISPR array structures remained relatively stable over time whereas others involved radical spacer acquisition during some periods, and diverse CRISPR arrays (associated with multiple isolates) co-existed in the same individuals with some persisted over time. Furthermore, features of CRISPR adaptation, evolution, and microdynamics were highlighted through an analysis of host-MGE network, such as modules of multiple MGEs and hosts, reflecting complex interactions between B. fragilis and its invaders mediated through the CRISPR-Cas systems. Conclusions We made available of all annotated CRISPR-Cas systems and their target MGEs, and their interaction network as a web resource at https://omics.informatics.indiana.edu/CRISPRone/Bfragilis. We anticipate it will become an important resource for studying of B. fragilis, its CRISPR-Cas systems, and its interaction with mobile genetic elements providing insights into evolutionary dynamics that may shape the species virulence and lead to its pathogenicity. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08770-8).
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Affiliation(s)
- Tony J Lam
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Kate Mortensen
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Yuzhen Ye
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA.
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Smith BJ, Piceno Y, Zydek M, Zhang B, Syriani LA, Terdiman JP, Kassam Z, Ma A, Lynch SV, Pollard KS, El-Nachef N. Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis. Sci Rep 2022; 12:5517. [PMID: 35365713 PMCID: PMC8976058 DOI: 10.1038/s41598-022-09307-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 03/16/2022] [Indexed: 01/04/2023] Open
Abstract
Fecal microbiota transplant is a promising therapy for ulcerative colitis. Parameters maximizing effectiveness and tolerability are not yet clear, and it is not known how import the transmission of donor microbes to patients is. Here (clinicaltrails.gov: NCT03006809) we have tested the effects of antibiotic pretreatment and compared two modes of maintenance dose delivery, capsules versus enema, in a randomized, pilot, open-label, 2 × 2 factorial design with 22 patients analyzed with mild to moderate UC. Clinically, the treatment was well-tolerated with favorable safety profile. Of patients who received antibiotic pretreatment, 6 of 11 experienced remission after 6 weeks of treatment, versus 2 of 11 non-pretreated patients (log odds ratio: 1.69, 95% confidence interval: −0.25 to 3.62). No significant differences were found between maintenance dosing via capsules versus enema. In exploratory analyses, microbiome turnover at both the species and strain levels was extensive and significantly more pronounced in the pretreated patients. Associations were also revealed between taxonomic turnover and changes in the composition of primary and secondary bile acids. Together these findings suggest that antibiotic pretreatment contributes to microbiome engraftment and possibly clinical effectiveness, and validate longitudinal strain tracking as a powerful way to monitor the dynamics and impact of microbiota transfer.
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Affiliation(s)
- Byron J Smith
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | | | - Martin Zydek
- Division of Gastroenterology, University of California, San Francisco, CA, USA
| | - Bing Zhang
- Division of Gastroenterology, University of California, San Francisco, CA, USA.,Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lara Aboud Syriani
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, USA
| | - Jonathan P Terdiman
- Division of Gastroenterology, University of California, San Francisco, CA, USA
| | | | - Averil Ma
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Susan V Lynch
- Division of Gastroenterology, University of California, San Francisco, CA, USA.,Benioff Center for Microbiome Medicine, University of California, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA. .,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Najwa El-Nachef
- Division of Gastroenterology, University of California, San Francisco, CA, USA.
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Segal JP, Mullish BH, Quraishi MN, Iqbal T, Marchesi JR, Sokol H. Mechanisms underpinning the efficacy of faecal microbiota transplantation in treating gastrointestinal disease. Therap Adv Gastroenterol 2020; 13:1756284820946904. [PMID: 32952613 PMCID: PMC7475788 DOI: 10.1177/1756284820946904] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 07/13/2020] [Indexed: 02/04/2023] Open
Abstract
Faecal microbiota transplantation (FMT) is currently a recommended therapy for recurrent/refractory Clostridioides difficile infection (CDI). The success of FMT for CDI has led to interest in its therapeutic potential in many other disorders. The mechanisms that underpin the efficacy of FMT are not fully understood. Importantly, FMT remains a crucial treatment in managing CDI and understanding the mechanisms that underpin its success will be critical to improve its clinical efficacy, safety and usability. Furthermore, a deeper understanding of this may allow us to expose FMT's full potential as a therapeutic tool for other disease states. This review will explore the current understanding of the mechanisms underlying the efficacy of FMT across a variety of diseases.
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Affiliation(s)
- Jonathan P. Segal
- Departments of Gastroenterology and Hepatology, St Mary’s Hospital, Imperial College Healthcare NHS Trust, South Wharf Rd, London W2 1NY, UK
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, UK
| | - Benjamin H. Mullish
- Departments of Gastroenterology and Hepatology, St Mary’s Hospital, Imperial College Healthcare NHS Trust, London, UK
- Department of Metabolism, Digestion and Reproduction, Division of Digestive Diseases, Imperial College London, UK
| | - Mohammed N. Quraishi
- University of Birmingham Microbiome Treatment Centre, University of Birmingham, Birmingham, UK
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Tariq Iqbal
- University of Birmingham Microbiome Treatment Centre, University of Birmingham, Birmingham, UK
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Julian R. Marchesi
- Department of Metabolism, Digestion and Reproduction, Division of Digestive Diseases, Imperial College London, UK
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Harry Sokol
- Gastroenterology Department, INSERM, Centre de Recherche Saint Antoine, CRSA, AP-HP, Sorbonne Université, Saint Antoine Hospital, Paris, France
- INRA, UMR1319 Micalis and AgroParisTech, Jouy en Josas, France Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France
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Van Rossum T, Ferretti P, Maistrenko OM, Bork P. Diversity within species: interpreting strains in microbiomes. Nat Rev Microbiol 2020; 18:491-506. [PMID: 32499497 DOI: 10.1038/s41579-020-0368-1] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2020] [Indexed: 02/06/2023]
Abstract
Studying within-species variation has traditionally been limited to culturable bacterial isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing and technical advances have enabled culture-free, high-resolution strain and subspecies analyses at high throughput and in complex environments. This holds great scientific promise but has also led to an overwhelming number of methods and terms to describe infraspecific variation. This Review aims to clarify these advances by focusing on the diversity within bacterial and archaeal species in the context of microbiomics. We cover foundational microevolutionary concepts relevant to population genetics and summarize how within-species variation can be studied and stratified directly within microbial communities with a focus on metagenomics. Finally, we describe how common applications of within-species variation can be achieved using metagenomic data. We aim to guide the selection of appropriate terms and analytical approaches to facilitate researchers in benefiting from the increasing availability of large, high-resolution microbiome genetic sequencing data.
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Affiliation(s)
- Thea Van Rossum
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Pamela Ferretti
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Oleksandr M Maistrenko
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany. .,Max Delbrück Centre for Molecular Medicine, Berlin, Germany. .,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany. .,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
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